ARTÍCULO

GTRAC: fast retrieval from compressedcollections of genomic variants

Autores: Tatwawadi, K. (Autor de correspondencia); Hernáez Arrazola, Mikel; Ochoa Álvarez, Idoia; Weissman, T.
Título de la revista: BIOINFORMATICS
ISSN: 1367-4803
Volumen: 32
Número: 17
Páginas: i479 - i486
Fecha de publicación: 2016
Resumen:
Motivation The dramatic decrease in the cost of sequencing has resulted in the generation of huge amounts of genomic data, as evidenced by projects such as the UK10K and the Million Veteran Project, with the number of sequenced genomes ranging in the order of 10 K to 1 M. Due to the large redundancies among genomic sequences of individuals from the same species, most of the medical research deals with the variants in the sequences as compared with a reference sequence, rather than with the complete genomic sequences. Consequently, millions of genomes represented as variants are stored in databases. These databases are constantly updated and queried to extract information such as the common variants among individuals or groups of individuals. Previous algorithms for compression of this type of databases lack efficient random access capabilities, rendering querying the database for particular variants and/or individuals extremely inefficient, to the point where compression is often relinquished altogether. Results We present a new algorithm for this task, called GTRAC, that achieves significant compression ratios while allowing fast random access over the compressed database. For example, GTRAC is able to compress a Homo sapiens dataset containing 1092 samples in 1.1¿GB (compression ratio of 160), while allowing for decompression of specific samples in less than a second and decompression of specific variants in 17¿ms. GTRAC uses and adapts techniques from information theory,